Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage

Abstract

The ultra-short DNA molecules still preserved in archeological remains can provide invaluable genetic information about past individuals, species, and communities within the half to 1-million-year time range. The sequence data are, however, generally affected by post-mortem DNA damage and include specific patterns of nucleotide misincorporations, which can help data authentication. Recent work in ancient mammals has shown that such patterns can also help assess past levels of DNA methylation in CpG contexts. Despite pioneering work in barley and sorghum, ancient epigenetic marks have received limited attention in plants and it remains unknown whether ancient epigenetic signatures can be retrieved in any of the three main sequence contexts (CG, CHG, and CHH). To address this question, we extended a statistical methylation score originally proposed to trace cytosine methylation in mammal sequence data to accommodate the three methylation contexts common in plants. We applied this score to a range of tissues (wood, cobs, and grains) and species (oak, maize, and barley), spanning both desiccated and waterlogged archeological samples. Ancient sequence data obtained for USER-treated DNA extracts yielded methylation scores on par with DNA methylation levels of modern organellar and nuclear genomes. At the quantitative level, scores were (1) positively correlated to post-mortem cytosine deamination, and (2) replicated relative contributions of CG, CHG, and CHH contexts to DNA methylation assessed by bisulfite DNA sequencing of modern plant tissues. This demonstrates that genuine DNA methylation signatures can be characterized in ancient plant remains, which opens new avenues for investigating the plant evolutionary response to farming, pollution, epidemics, and changing environmental conditions.

Investigating food production‐associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise

“…Applying their algorithm to published ancient human genomes, these authors showed tissue‐based clustering among at least some paleomethylomes they analyzed. Successful retrieval of paleomethylation signatures has also been reported for other species, including barley, maize, and horses (Liu et al., 2023 ; Smith et al., 2014 ; Wagner et al., 2020 ).…”

“…Applying their algorithm to published ancient human genomes, these authors showed tissue-based clustering among at least some paleomethylomes they analyzed. Successful retrieval of paleomethylation signatures has also been reported for other species, including barley, maize, and horses (Liu et al, 2023;Smith et al, 2014;Wagner et al, 2020). Despite the promising results described above, whether lifestylerelated paleomethylation signatures may be retrievable from ancient bone and tooth material remains unknown.…”

Investigating DNA methylation changes associated with food production using paleogenomes

“…Applying their algorithm to published ancient human genomes, these authors showed tissue-based clustering among at least some of the paleomethylomes they analysed. Successful retrieval of paleomethylation signatures has also been reported for other species, including barley, maize, and horses (Wagner et al, 2020;Smith et al, 2014;Liu et al, 2023).…”

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

“…Before proceeding to downstream analyses, the variant calls are subjected to several filtering steps. Methylated CpG sites are protected from UDG enzyme treatments and so post-mortem damage might remain in such sites [ 35 , 36 ]. Ideally, a variant filter should therefore capture sites in ancient/historical samples that have a basepair change from CpG due to post-mortem damage.…”